An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070508/ 5cabdaac/attachment.pl

affyio is outdated. b On May 8, 2007, at 10:52 AM, Stephen Henderson wrote: > Hello > I've just updated my version of R and Bioconductor using the > BiocLite script. > I now find I cannot create an AffyBatch object: > >> dir() > [1] "GSM137899.CEL.gz" "GSM138009.CEL.gz" "GSM138010.CEL.gz" > >> ReadAffy()->pv.bat > Error in read.affybatch(filenames = l$filenames, phenoData = l > $phenoData, : > VECTOR_ELT() can only be applied to a 'list', not a 'char' > > > Does anyone know why? Oh and justRMA gives the same error. > > > Here is my sessioninfo() > >> sessionInfo() > R version 2.5.0 (2007-04-23) > i686-pc-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US > .UTF-8;LC_ > MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N > AME=C;LC_A > DDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] "tools" "stats" "graphics" "grDevices" "utils" > "datasets" > [7] "methods" "base" > > other attached packages: > affy affyio Biobase > "1.14.0" "1.0.0" "1.14.0" > > ********************************************************************** > This email and any files transmitted with it are confidentia... > {{dropped}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor

Hmmm-- yes updating that seems to work. Not sure how I did that. Thanks Stephen Henderson Wolfson Inst. for Biomedical Research Cruciform Bldg., Gower Street University College London United Kingdom, WC1E 6BT +44 (0)207 679 6827 -----Original Message----- From: Benilton Carvalho [mailto:bcarvalh@jhsph.edu] Sent: 08 May 2007 16:12 To: Stephen Henderson Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] ReadAffy problem affyio is outdated. b On May 8, 2007, at 10:52 AM, Stephen Henderson wrote: > Hello > I've just updated my version of R and Bioconductor using the > BiocLite script. > I now find I cannot create an AffyBatch object: > >> dir() > [1] "GSM137899.CEL.gz" "GSM138009.CEL.gz" "GSM138010.CEL.gz" > >> ReadAffy()->pv.bat > Error in read.affybatch(filenames = l$filenames, phenoData = l > $phenoData, : > VECTOR_ELT() can only be applied to a 'list', not a 'char' > > > Does anyone know why? Oh and justRMA gives the same error. > > > Here is my sessioninfo() > >> sessionInfo() > R version 2.5.0 (2007-04-23) > i686-pc-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US > .UTF-8;LC_ > MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N > AME=C;LC_A > DDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] "tools" "stats" "graphics" "grDevices" "utils" > "datasets" > [7] "methods" "base" > > other attached packages: > affy affyio Biobase > "1.14.0" "1.0.0" "1.14.0" > > ********************************************************************** > This email and any files transmitted with it are confidentia... > {{dropped}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor ********************************************************************** This email and any files transmitted with it are confidentia...{{dropped}}